*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
Quoting Ethan Merritt <[EMAIL PROTECTED]>: > > If this concept is taken further, one could ask why we are not > > explicitly refining hydrogen atoms ? > > We are. > At least, those who correctly use available options in refmac or shelx are. > The best results (R, Rfree, geometry) are obtained by explicit inclusion > of hydrogens via the riding-hydrogen model. This is also a basis for the > Molprobity validation tools. This misses the point. In the riding hydrogen model, the positions of the hydrogens are NOT explicitly refined but extrapolated in each refinement cycle from knowledge of the positions of the other protein atoms and by assuming ideal geometry. The riding hydrogen model does indeed improve the geometry and R-factors, but I guess that not many people would write out and deposit a PDB file with hydrogens for a 3A structure, even if they used the riding hydrogen model during the refinement. > In fact the hydrogen scattering contribution falls off with > resolution just like the normal scattering from any other atom type. Did anyone on this bulletin board claim the contrary ? In fact the hydrogen scattering curve falls off slightly faster than that of carbon. But this also misses the point. With ultra-high resolution data, the non-hydrogen part of the structure can be refined well enough so that hydrogen atoms show up in difference density maps. With low-resolution data this is not the case. A similar reasoning probably holds for disordered side-chains. Marc Schiltz
